# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 16:09:13 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CNC(=O)CCCC/C=C/C(C)C)ccc1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 4DY  4DY  (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide  ligand  49  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4DY
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 4DY  C1   C  CR6   0   0.119    3.5617  -0.6298   1.2024
 4DY  C2   C  CR16  0  -0.421    3.9151   0.4155   0.3432
 4DY  C3   C  CR6   0   0.315    5.0181   0.3058  -0.4846
 4DY  C4   C  CR6   0   0.271    5.7974  -0.8655  -0.4656
 4DY  C5   C  CR16  0  -0.334    5.4477  -1.8957   0.3867
 4DY  C40  C  CH3   0  -0.646   -8.2088  -1.7966  -1.2212
 4DY  C38  C  CH1   0  -0.303   -8.0508  -0.2836  -1.0676
 4DY  C44  C  CH3   0  -0.645   -9.3326   0.3367  -0.5108
 4DY  C37  C  C1    0  -0.183   -6.8794   0.0371  -0.1877
 4DY  C36  C  C1    0  -0.219   -5.8051   0.7250  -0.5623
 4DY  C33  C  CH2   0  -0.480   -4.6216   1.0204   0.3038
 4DY  C30  C  CH2   0  -0.417   -3.3450   0.3636  -0.2227
 4DY  C27  C  CH2   0  -0.418   -2.1166   0.7092   0.6078
 4DY  C24  C  CH2   0  -0.565   -0.8605   0.0175   0.0856
 4DY  C22  C  C     0   0.565    0.3730   0.3923   0.8775
 4DY  O23  O  O     0  -0.511    0.6705   1.5619   1.0898
 4DY  N21  N  NH1   0  -0.621    1.1010  -0.6429   1.3286
 4DY  C17  C  CH2   0  -0.398    2.3370  -0.5089   2.0719
 4DY  C6   C  CR16  0  -0.324    4.3350  -1.7776   1.2160
 4DY  O10  O  OH1   0  -0.632    6.8784  -0.9998  -1.2614
 4DY  O12  O  O2    0  -0.489    5.4457   1.2517  -1.3489
 4DY  C13  C  CH3   0  -0.432    4.6901   2.4387  -1.4805
 4DY  H2   H  HCR6  0   0.275    3.3118   1.3145   0.3370
 4DY  H5   H  HCR6  0   0.263    6.0484  -2.7969   0.3994
 4DY  H40  H  HCH3  0   0.215   -8.4073  -2.2695  -0.2564
 4DY  H6T  H  HCH3  0   0.226   -9.0418  -2.0367  -1.8847
 4DY  H6S  H  HCH3  0   0.227   -7.3085  -2.2516  -1.6359
 4DY  H38  H  HCH1  0   0.228   -7.8622   0.1431  -2.0586
 4DY  H6U  H  HCH3  0   0.215   -9.5514  -0.0509   0.4867
 4DY  H6V  H  HCH3  0   0.227   -9.2504   1.4217  -0.4367
 4DY  H44  H  HCH3  0   0.225  -10.1875   0.1075  -1.1500
 4DY  H37  H  H     0   0.224   -6.9371  -0.3366   0.8350
 4DY  H36  H  H     0   0.226   -5.7499   1.0927  -1.5861
 4DY  H33  H  HCH2  0   0.225   -4.4650   2.1038   0.3529
 4DY  H6R  H  HCH2  0   0.227   -4.8121   0.6854   1.3275
 4DY  H6Q  H  HCH2  0   0.219   -3.4851  -0.7216  -0.2424
 4DY  H30  H  HCH2  0   0.218   -3.1801   0.6696  -1.2614
 4DY  H27  H  HCH2  0   0.226   -1.9658   1.7912   0.6053
 4DY  H6P  H  HCH2  0   0.226   -2.2853   0.4197   1.6499
 4DY  H6O  H  HCH2  0   0.245   -1.0087  -1.0648   0.0785
 4DY  H24  H  HCH2  0   0.260   -0.6869   0.3144  -0.9534
 4DY  H21  H  HNH1  0   0.399    0.8147  -1.5754   1.0797
 4DY  H6N  H  HCH2  0   0.268    2.3529  -1.2847   2.8383
 4DY  H17  H  HCH2  0   0.262    2.3224   0.4496   2.5898
 4DY  H6   H  HCR6  0   0.249    4.0785  -2.5969   1.8767
 4DY  H10  H  HOH1  0   0.471    6.9888  -0.2119  -1.8073
 4DY  H6M  H  HCH3  0   0.230    3.6668   2.2331  -1.8052
 4DY  H6L  H  HCH3  0   0.231    4.6578   3.0052  -0.5465
 4DY  H13  H  HCH3  0   0.263    5.1855   3.0401  -2.2384

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 4DY  C40  C38  single    1.529  0.020  1.529
 4DY  C30  C33  single    1.529  0.020  1.529
 4DY  C30  C27  single    1.523  0.020  1.523
 4DY  C37  C38  single    1.500  0.020  1.500
 4DY  C37  C36  double    1.329  0.020  1.329
 4DY  C33  C36  single    1.496  0.020  1.496
 4DY  C38  C44  single    1.529  0.020  1.529
 4DY  C24  C27  single    1.526  0.020  1.526
 4DY  C24  C22  single    1.513  0.020  1.513
 4DY  C5   C6   aromatic  1.393  0.020  1.393
 4DY  C5   C4   aromatic  1.382  0.020  1.382
 4DY  C6   C1   aromatic  1.384  0.020  1.384
 4DY  N21  C22  single    1.344  0.020  1.344
 4DY  N21  C17  single    1.448  0.020  1.448
 4DY  C22  O23  double    1.225  0.020  1.225
 4DY  O10  C4   single    1.349  0.020  1.349
 4DY  C4   C3   aromatic  1.407  0.020  1.407
 4DY  C1   C17  single    1.507  0.020  1.507
 4DY  C1   C2   aromatic  1.398  0.020  1.398
 4DY  C3   C2   aromatic  1.384  0.020  1.384
 4DY  C3   O12  single    1.351  0.020  1.351
 4DY  O12  C13  single    1.413  0.020  1.413
 4DY  C2   H2   single    0.930  0.020  1.080
 4DY  C5   H5   single    0.930  0.020  1.080
 4DY  C40  H40  single    0.970  0.020  1.090
 4DY  C40  H6T  single    0.970  0.020  1.090
 4DY  C40  H6S  single    0.970  0.020  1.090
 4DY  C38  H38  single    0.970  0.020  1.090
 4DY  C44  H6U  single    0.970  0.020  1.090
 4DY  C44  H6V  single    0.970  0.020  1.090
 4DY  C44  H44  single    0.970  0.020  1.090
 4DY  C37  H37  single    0.930  0.020  1.080
 4DY  C36  H36  single    0.930  0.020  1.080
 4DY  C33  H33  single    0.970  0.020  1.090
 4DY  C33  H6R  single    0.970  0.020  1.090
 4DY  C30  H6Q  single    0.970  0.020  1.090
 4DY  C30  H30  single    0.970  0.020  1.090
 4DY  C27  H27  single    0.970  0.020  1.090
 4DY  C27  H6P  single    0.970  0.020  1.090
 4DY  C24  H6O  single    0.970  0.020  1.090
 4DY  C24  H24  single    0.970  0.020  1.090
 4DY  N21  H21  single    0.860  0.020  1.020
 4DY  C17  H6N  single    0.970  0.020  1.090
 4DY  C17  H17  single    0.970  0.020  1.090
 4DY  C6   H6   single    0.930  0.020  1.080
 4DY  O10  H10  single    0.850  0.020  0.980
 4DY  C13  H6M  single    0.970  0.020  1.090
 4DY  C13  H6L  single    0.970  0.020  1.090
 4DY  C13  H13  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 4DY  C6   C1   C17  121.00  3.000
 4DY  C17  C1   C2   120.00  3.000
 4DY  C6   C1   C2   118.99  3.000
 4DY  H2   C2   C3   120.44  3.000
 4DY  H2   C2   C1   118.91  3.000
 4DY  C3   C2   C1   120.66  3.000
 4DY  O12  C3   C4   114.60  3.000
 4DY  O12  C3   C2   125.43  3.000
 4DY  C4   C3   C2   119.97  3.000
 4DY  O10  C4   C5   119.49  3.000
 4DY  O10  C4   C3   121.25  3.000
 4DY  C5   C4   C3   119.26  3.000
 4DY  H5   C5   C6   120.44  3.000
 4DY  H5   C5   C4   119.16  3.000
 4DY  C6   C5   C4   120.40  3.000
 4DY  H6S  C40  H6T  107.88  3.000
 4DY  H6S  C40  H40  107.77  3.000
 4DY  H6T  C40  H40  107.63  3.000
 4DY  H6S  C40  C38  111.45  3.000
 4DY  H6T  C40  C38  110.95  3.000
 4DY  H40  C40  C38  111.00  3.000
 4DY  H38  C38  C37  108.24  3.000
 4DY  H38  C38  C44  108.41  3.000
 4DY  C37  C38  C44  110.76  3.000
 4DY  H38  C38  C40  108.21  3.000
 4DY  C44  C38  C40  110.57  3.000
 4DY  C37  C38  C40  110.56  3.000
 4DY  H44  C44  H6V  107.93  3.000
 4DY  H44  C44  H6U  107.65  3.000
 4DY  H6V  C44  H6U  107.82  3.000
 4DY  H44  C44  C38  110.98  3.000
 4DY  H6V  C44  C38  111.42  3.000
 4DY  H6U  C44  C38  110.89  3.000
 4DY  H37  C37  C36  118.97  3.000
 4DY  H37  C37  C38  115.83  3.000
 4DY  C36  C37  C38  125.20  3.000
 4DY  H36  C36  C33  115.94  3.000
 4DY  H36  C36  C37  118.72  3.000
 4DY  C33  C36  C37  125.33  3.000
 4DY  H6R  C33  H33  106.61  3.000
 4DY  H6R  C33  C30  109.64  3.000
 4DY  H33  C33  C30  108.71  3.000
 4DY  H6R  C33  C36  110.09  3.000
 4DY  H33  C33  C36  109.53  3.000
 4DY  C30  C33  C36  112.10  3.000
 4DY  H30  C30  H6Q  106.22  3.000
 4DY  H30  C30  C27  109.42  3.000
 4DY  H6Q  C30  C27  109.76  3.000
 4DY  H30  C30  C33  109.41  3.000
 4DY  H6Q  C30  C33  108.98  3.000
 4DY  C27  C30  C33  112.84  3.000
 4DY  H6P  C27  H27  106.58  3.000
 4DY  H6P  C27  C24  109.44  3.000
 4DY  H27  C27  C24  109.54  3.000
 4DY  H6P  C27  C30  109.57  3.000
 4DY  H27  C27  C30  109.57  3.000
 4DY  C24  C27  C30  112.00  3.000
 4DY  H24  C24  H6O  106.50  3.000
 4DY  H24  C24  C22  107.48  3.000
 4DY  H6O  C24  C22  111.06  3.000
 4DY  H24  C24  C27  109.42  3.000
 4DY  H6O  C24  C27  109.86  3.000
 4DY  C22  C24  C27  112.32  3.000
 4DY  N21  C22  O23  123.07  3.000
 4DY  O23  C22  C24  121.67  3.000
 4DY  N21  C22  C24  115.26  3.000
 4DY  H21  N21  C17  117.08  3.000
 4DY  H21  N21  C22  118.46  3.000
 4DY  C17  N21  C22  124.29  3.000
 4DY  H17  C17  H6N  106.97  3.000
 4DY  H17  C17  N21  108.29  3.000
 4DY  H6N  C17  N21  107.89  3.000
 4DY  H17  C17  C1   110.84  3.000
 4DY  H6N  C17  C1   109.67  3.000
 4DY  N21  C17  C1   112.96  3.000
 4DY  H6   C6   C5   119.22  3.000
 4DY  H6   C6   C1   120.06  3.000
 4DY  C5   C6   C1   120.72  3.000
 4DY  H10  O10  C4   110.12  3.000
 4DY  C13  O12  C3   118.59  3.000
 4DY  H13  C13  H6L  108.82  3.000
 4DY  H13  C13  H6M  108.89  3.000
 4DY  H6L  C13  H6M  108.89  3.000
 4DY  H13  C13  O12  106.62  3.000
 4DY  H6L  C13  O12  111.81  3.000
 4DY  H6M  C13  O12  111.73  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 4DY  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 4DY  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 4DY  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 4DY  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 4DY  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 4DY  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 4DY  CONST_07  O12  C3   C2   C1    180.00   0.0  0
 4DY  CONST_08  O10  C4   C3   C2    180.00   0.0  0
 4DY  CONST_09  C17  C1   C2   C3    180.00   0.0  0
 4DY  CONST_10  C17  C1   C6   C5    180.00   0.0  0
 4DY  CONST_11  O12  C3   C4   C5    180.00   0.0  0
 4DY  CONST_12  O10  C4   C5   C6    180.00   0.0  0
 4DY  CONST_13  H5   C5   C6   C1    180.00   0.0  0
 4DY  CONST_14  H6   C6   C1   C2    180.00   0.0  0
 4DY  CONST_15  H2   C2   C3   C4    180.00   0.0  0
 4DY  CONST_16  C17  N21  C22  C24   180.00   0.0  0
 4DY  CONST_17  C17  N21  C22  O23     0.00   0.0  0
 4DY  CONST_18  H21  N21  C22  C24     0.00   0.0  0
 4DY  Var_01    N21  C17  C1   C2     73.58  30.0  2
 4DY  Var_02    C22  N21  C17  C1    -96.70  30.0  1
 4DY  Var_03    H6M  C13  O12  C3    -59.40  30.0  3
 4DY  Var_04    C33  C36  C37  C38  -178.55   0.0  2
 4DY  Var_05    C36  C37  C38  C40   118.47  30.0  1
 4DY  Var_06    C30  C33  C36  C37   116.03  30.0  1
 4DY  Var_07    C27  C30  C33  C36   177.18  30.0  2
 4DY  Var_08    C24  C27  C30  C33   178.63  30.0  3
 4DY  Var_09    C22  C24  C27  C30   178.08  30.0  2
 4DY  Var_10    N21  C22  C24  C27   128.28  30.0  3
 4DY  Var_11    H6U  C44  C38  C40    62.39  30.0  3
 4DY  Var_12    H40  C40  C38  C44   -60.97  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 4DY  plan-1  C1   0.020
 4DY  plan-1  C2   0.020
 4DY  plan-1  C3   0.020
 4DY  plan-1  C4   0.020
 4DY  plan-1  C5   0.020
 4DY  plan-1  C17  0.020
 4DY  plan-1  C6   0.020
 4DY  plan-1  O10  0.020
 4DY  plan-1  O12  0.020
 4DY  plan-1  H2   0.020
 4DY  plan-1  H5   0.020
 4DY  plan-1  H6   0.020
 4DY  plan-2  C24  0.020
 4DY  plan-2  C22  0.020
 4DY  plan-2  O23  0.020
 4DY  plan-2  N21  0.020
 4DY  plan-2  C17  0.020
 4DY  plan-2  H21  0.020
 4DY  plan-3  C38  0.020
 4DY  plan-3  C37  0.020
 4DY  plan-3  C36  0.020
 4DY  plan-3  C33  0.020
 4DY  plan-3  H37  0.020
 4DY  plan-3  H36  0.020

